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I am testing a 10x fastq dataset , but cellranger count complains "An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input", I have tried all the chemistry recommendation codes on the 10x genomics website, and I still get the same result, how can I solve this problem, thanks.

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  • $\begingroup$ It is difficult to provide an answer when the question does not include what the input is, what command was run, ... I can only suggest to use the --chemistry=auto option of cellranger count. $\endgroup$
    – haci
    Dec 12, 2021 at 14:03
  • $\begingroup$ What does the quality look like on those reads? If this is 10XGenomics library, they should be able to help your troubleshoot. $\endgroup$
    – swbarnes2
    Dec 12, 2021 at 22:44
  • $\begingroup$ Could you please give a few more details about the nature of this project? Are you sure this is a single-cell dataset (I'm aware that 10X do other non-single-cell things as well)? Showing the first few lines of header from the fastq files can be very helpful to work out the structure of the experiment. $\endgroup$
    – gringer
    Dec 12, 2021 at 23:41
  • $\begingroup$ how were your fastqs generated? and how are they named? $\endgroup$ Dec 13, 2021 at 21:01
  • $\begingroup$ Thanks @ciwei for providing your answer. Could you kindly check the "accept" box for your answer? This does help site statistics $\endgroup$
    – M__
    Sep 2, 2023 at 13:34

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I have solve this problem, cause the combined barcode is differernt from the common 10x barcode. when mapping the genome, need to add-- chemistry ARC-v1 when cellranger count.

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    $\begingroup$ Excuse me, how do you determine the required chemistry? $\endgroup$
    – JY_sea
    Apr 6, 2022 at 6:10
  • $\begingroup$ ARC-v1 means this was done using a multiomic kit. From cellranger count --help "To analyze the GEX portion of multiome data, chemistry must be set to 'ARC-v1'; 'ARC-v1' chemistry cannot be autodetected" $\endgroup$
    – nico
    Nov 1, 2023 at 16:44
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Answer from @maximilian-press, converted from comments:

I can't comment on 10X data specifically, however, I suggest writing a simple script or command that counts the frequency of each barcode, and reports back the N (10? 20? 100?) most frequent ones, which will allow you to investigate in more detail. This is what I have done in the case of suspected bardode swaps or reverse complement issues.

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